System Maintenance & Administration

Adding a new user or developer account

User accounts on the RTC, ICC, and AOC machines are members of magaox. Developer accounts are additionally members of magaox-dev and wheel.

/opt/MagAOX/source/MagAOX/setup/ contains scripts to help you remember which groups and what permissions the ~/.ssh folder should have.

add_a_user.sh

Creates a new user account in the group magaox, creates .ssh (u=rwx,g=r,o=r), and .ssh/authorized_keys (u=rw,g=,o=).

Example:

$ /opt/MagAOX/source/MagAOX/setup/add_a_user.sh klmiller

add_a_developer.sh

Just like add_a_user.sh (in fact, uses it). Additionally adds the new account to the wheel (RTC/ICC) or sudo (AOC) group and magaox-dev groups.

Configuring git for a new user account

We use GitHub Personal Access Tokens coupled with HTTPS push to synchronize changes on the instrument. Configuration is required for your credentials to be remembered.

  1. Log in to the computer (AOC, RTC, ICC, vm, etc) where you want to configure git

  2. Change directories to a repository (e.g. cd /opt/MagAOX/calib) and verify it is set up for HTTPS push:

    $ cd /opt/MagAOX/calib
    $ git remote -v
    origin   https://github.com/magao-x/calib.git (fetch)
    origin   https://github.com/magao-x/calib.git (push)
    
  3. If you haven’t already for this machine, configure your name and email address:

    $ git config --global user.email "youremailusernamehere@youremaildomainhere.com"
    $ git config --global user.name "Your Name Here"
    
  4. Configure the ‘store’ credential helper, which will store your credentials so you do not have to re-enter them:

    $ git config --global credential.helper store
    
  5. Create (or retrieve from your password manager) a GitHub Personal Access Token. If you don’t have one, log in to GitHub and visit https://github.com/settings/tokens.

  6. Attempt to push, and enter/paste your username and personal access token as password:

    $ git push
    Username for 'https://github.com/magao-x/calib.git': your-github-user-name
    Password for 'https://your-github-user-name@github.com/magao-x/calib.git':
    

    (Note that even if you don’t see it, your key is being entered.)

  7. Attempt to push again. You should not be prompted for credentials a second time.

Upgrading NVIDIA CUDA and drivers

The CUDA install script at https://github.com/magao-x/MagAOX/blob/master/setup/steps/install_cuda.sh will install CUDA on a new system (provided that pre_provision.sh is run first, and the system is rebooted).

Upgrading CUDA is more involved, as the systems stubbornly insist on loading the driver even when asked nicely not to, and the installer won’t work if the driver is loaded.

  1. (on AOC only) Default to text-based boot: systemctl set-default multi-user.target

  2. Disable all the driver modules.

    Open /etc/default/grub and append the following to the line beginning GRUB_CMDLINE_LINUX_DEFAULT (inside the quotes):

    nvidia_modeset.blacklist=1 nvidia_uvm.blacklist=1 nvidia.blacklist=1 rd.driver.blacklist=nvidia_modeset,nvidia_uvm,nvidia
    
  3. Install the new config with sudo grub2-mkconfig -o /boot/grub2/grub.cfg

  4. Reboot, verify with lsmod | grep nv that no driver modules loaded

  5. Use sudo /usr/bin/nvidia-uninstall to uninstall the driver (choosing “No” when asked whether to “attempt restoration of the original X configuration file”)

  6. Use sudo /usr/local/cuda/bin/cuda-uninstaller to uninstall CUDA (checking all available options before choosing “Done”)

  7. Remove the boot options that disable the driver.

    Open /etc/default/grub and remove the added options from GRUB_CMDLINE_LINUX_DEFAULT.

  8. Install the new config with sudo grub2-mkconfig -o /boot/grub2/grub.cfg

  9. Reboot again! Verify no driver is loaded again!

  10. Install CUDA using sudo bash -x /opt/MagAOX/source/MagAOX/setup/steps/install_cuda.sh

  11. (on AOC only) Default to graphical boot again with systemctl set-default graphical.target and complete boot to graphical desktop with systemctl isolate graphical.target

  12. Rebuild MAGMA with the new version of CUDA:

cd /opt/MagAOX/vendor/magma-X.Y.Z
make clean
make -j 32
make install

Upgrading the RT kernel

The CentOS 7 RT kernel includes backported patches from the mainline kernel to 3.10.0 where CentOS 7 was frozen, plus the PREEMPT RT patch set and bug fixes from newer versions of that. On occasion a new version will appear in the CentOS 7 RT package repository and it may be worth upgrading to see if any of our bugs are fixed.

  1. Remove versionlock (if any): yum versionlock delete kernel-rt

  2. sudo yum update kernel-rt kernel-rt-devel

  3. Reboot, verify new version in uname -a

  4. Reinstall drivers with kernel modules:

    • NVIDIA (all machines)

      1. sudo /usr/bin/nvidia-uninstall

      2. cd /opt/MagAOX/vendor/cuda and bash cuda_11.1.1_455.32.00_linux.run --extract=/tmp/cuda11 (or as appropriate for the version of CUDA you have)

      3. Become root: /usr/bin/sudo -i

      4. cd /tmp/cuda11

      5. Verify realpath $(which cc) is /usr/bin/gcc (and not the DevToolset-7 one)

      6. export IGNORE_PREEMPT_RT_PRESENCE=1

      7. Run the installer: bash NVIDIA-Linux-x86_64-455.32.00.run

      8. On next reboot, verify nvidia-smi works and shows all cards

    • EDT (RTC, ICC)

      1. cd /opt/MagAOX/source/MagAOX/setup/steps

      2. sudo mv /opt/EDTpdv /opt/EDTpdv.oldkernel

      3. sudo bash install_edt.sh

    • ALPAO (RTC, ICC)

      1. cd /opt/MagAOX/source/MagAOX/setup/steps

      2. sudo bash install_alpao.sh

    • BMC (RTC)

      1. cd /opt/MagAOX/vendor/bmc

      2. sudo bash install.sh

    • Andor (ICC)

      1. cd /opt/MagAOX/source/MagAOX/setup/steps

      2. bash install_andor.sh

  5. Reboot, verify hardware is working (e.g. nvidia-smi, cameras all connecting, etc)